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endonuclease

Euk-Vir

Noumeavirus

endonuclease__YP_009345303__Noumeavirus__1955558

Identity

Accession:
YP_009345303 ↗
Protein ID:
endonuclease
Kingdom:
euk

Quality

76.6 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Marseilleviridae› Marseillevirus› Noumeavirus

TaxID: 1955558

Cluster

View cluster (7 members)

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 414-544
PDB
Domain cluster: rep: IMGVR_UViG_3300025584_000284-3300025584-Ga0209774_100031726__D151-252
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24308.2 best DUF7487 172.6 1.60e-50 85.5% 49.5%
D2 medium residues 3-77
PDB
Domain cluster: rep: NC_031022.1__YP_009280252.1__BI056_gp065__00065__D70-126
D3 medium residues 200-250
PDB
Domain cluster: rep: MutH_Vsr_archaeal_HJR-like_endonuclease__YP_003406987__Marseillevirus_marseillevirus__694581__D84-138
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3pg1A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.66 53.0 4.09e-01 94.1% 93.8%
2e6nA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.66 50.0 4.04e-01 84.3% 48.1%
7cfdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.65 51.0 4.53e-01 86.3% 68.5%
2mamA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.64 51.0 4.00e-01 94.1% 92.4%
2wfwB02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.63 43.0 3.95e-01 70.6% 85.1%
4fssB00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.62 48.0 4.61e-01 86.3% 93.4%
4ytlA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.62 49.0 4.93e-01 88.2% 96.0%
2ckkA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.62 48.0 4.77e-01 86.3% 94.3%
1zuyA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.61 44.0 4.34e-01 80.4% 96.6%
2yrrA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.61 51.0 4.06e-01 98.0% 78.4%
1csnA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.61 41.0 2.75e-01 70.6% 30.8%
1tu5A01 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 52.0 4.17e-01 100.0% 80.6%
1evlA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.61 50.0 4.07e-01 100.0% 76.8%
4hwtA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.61 49.0 4.03e-01 98.0% 71.8%
1b8gA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.60 51.0 3.67e-01 100.0% 56.1%
2e7jA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.60 50.0 4.04e-01 100.0% 79.5%
2mj7A00 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.60 47.0 3.56e-01 92.2% 56.7%
1n27A00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.59 47.0 3.84e-01 88.2% 60.4%
4fw1A02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.59 43.0 4.25e-01 80.4% 85.2%
3luuA00 3.30.2020.30 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › 0.59 47.0 4.06e-01 94.1% 93.3%
1awoA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.59 45.0 4.37e-01 86.3% 94.7%
3rauA00 1.25.40.280 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › alix/aip1 like domains 0.58 42.0 2.63e-01 82.4% 44.4%
1bkbA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 42.0 3.96e-01 80.4% 75.4%
1svvB02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.58 46.0 3.92e-01 94.1% 80.4%
3aqqA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 41.0 3.45e-01 80.4% 49.5%
1ob8A00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.58 47.0 3.76e-01 100.0% 92.4%
2k5nA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 41.0 3.76e-01 80.4% 64.9%
3b46A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.57 46.0 3.36e-01 98.0% 63.3%
2z61A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.56 47.0 3.45e-01 100.0% 51.6%
1vgyA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.55 45.0 2.98e-01 100.0% 38.7%
2vnuD04 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.55 45.0 4.06e-01 98.0% 87.3%
4q66D01 6.20.120.50 Special › Other non-globular › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.55 40.0 3.60e-01 80.4% 60.3%
2zw5A02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.55 43.0 3.51e-01 98.0% 87.4%
4c5wA01 3.30.2020.30 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › 0.54 43.0 3.62e-01 94.1% 92.8%
3hdcA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 38.0 3.00e-01 78.4% 82.8%
4opmA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 45.0 2.86e-01 100.0% 21.4%
3t4nA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.54 43.0 3.67e-01 96.1% 87.5%
4pmwA04 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 42.0 3.64e-01 98.0% 87.9%
1o4sA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 42.0 3.19e-01 100.0% 53.0%
3rriA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.51 40.0 3.23e-01 100.0% 80.2%
3vlaA02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.51 37.0 2.53e-01 80.4% 34.1%
4le7A01 2.90.10.30 Mainly Beta › Orthogonal Prism › Agglutinin, subunit A › 0.51 39.0 2.93e-01 98.0% 96.5%
ECOD (43)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5081654 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.82 71.0 6.74e-01 100.0% 83.3%
3776390 4.1.1.91 ↗ beta barrels › SH3 › SH3 › SH3 › hSH3 0.66 49.0 3.74e-01 80.4% 47.8%
3605643 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.66 56.0 3.41e-01 100.0% 34.9%
4238704 6020.1.1.1 ↗ a+b two layers › Beta domain of DivIB/FtsQ › Beta domain of DivIB/FtsQ › Beta domain of DivIB/FtsQ › FtsQ_DivIB_C 0.66 57.0 4.33e-01 100.0% 45.6%
3841524 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.66 49.0 3.79e-01 80.4% 50.0%
3939132 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.65 51.0 4.18e-01 88.2% 68.0%
3949346 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.64 47.0 3.54e-01 76.5% 31.2%
4453273 6020.1.1.1 ↗ a+b two layers › Beta domain of DivIB/FtsQ › Beta domain of DivIB/FtsQ › Beta domain of DivIB/FtsQ › FtsQ_DivIB_C 0.64 54.0 3.99e-01 100.0% 50.3%
4646598 6020.1.1.1 ↗ a+b two layers › Beta domain of DivIB/FtsQ › Beta domain of DivIB/FtsQ › Beta domain of DivIB/FtsQ › FtsQ_DivIB_C 0.64 54.0 4.13e-01 100.0% 46.1%
3970545 310.3.1.2 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › T2SSM 0.62 45.0 4.05e-01 82.4% 91.1%
3598389 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.61 52.0 4.03e-01 100.0% 89.2%
3301527 3016.1.1.1 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_1_2 0.61 51.0 3.56e-01 100.0% 49.7%
5040873 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.60 49.0 3.35e-01 98.0% 33.0%
1152753 3016.1.1.1 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_1_2 0.59 48.0 3.88e-01 100.0% 77.3%
4963580 4.1.1.40 ↗ beta barrels › SH3 › SH3 › SH3 › FeoA 0.59 46.0 4.03e-01 88.2% 83.7%
4113970 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.59 47.0 3.88e-01 96.1% 81.7%
5062937 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.58 47.0 3.80e-01 96.1% 86.4%
3253321 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.58 41.0 3.93e-01 80.4% 89.2%
3252596 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.58 47.0 3.63e-01 98.0% 87.7%
4259370 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 42.0 4.17e-01 80.4% 81.8%
4016123 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 48.0 2.99e-01 100.0% 60.6%
3606563 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.57 46.0 3.60e-01 98.0% 78.5%
3881061 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.57 47.0 4.41e-01 94.1% 93.8%
None — 0.56 41.0 3.77e-01 80.4% 72.9%
3645592 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.56 46.0 3.85e-01 98.0% 92.0%
3495622 3246.1.1.3 ↗ few secondary structure elements › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins › ADAMTS_CR_2 0.56 40.0 3.70e-01 82.4% 64.0%
4299504 1013.1.1.1 ↗ beta duplicates or obligate multimers › WD repeat-containing protein 48 ancillary domain › WD repeat-containing protein 48 ancillary domain › WD repeat-containing protein 48 ancillary domain › DUF3337 0.56 45.0 3.17e-01 100.0% 65.0%
3336463 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.55 46.0 4.04e-01 94.1% 66.7%
4284398 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.55 39.0 3.98e-01 76.5% 78.0%
3287428 211.1.1.11 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase_6 0.55 39.0 3.16e-01 82.4% 34.8%
5044374 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.54 39.0 3.86e-01 80.4% 98.2%
3757952 3246.1.1.3 ↗ few secondary structure elements › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins › ADAMTS_CR_2 0.54 39.0 3.50e-01 82.4% 56.2%
5017134 208.1.1.1 ↗ beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Trimeric LpxA-like enzymes › Trimeric LpxA-like enzymes › Hexapep 0.54 37.0 2.58e-01 74.5% 22.1%
5018121 211.1.1.1 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase 0.54 39.0 3.90e-01 80.4% 76.4%
5033076 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.54 40.0 3.93e-01 82.4% 89.1%
5012656 330.5.1.0 ↗ a+b two layers › dsRBD-like › Bacillus phage protein › Bacillus phage protein 0.53 43.0 3.76e-01 98.0% 76.5%
3898264 3246.1.1.0 ↗ few secondary structure elements › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins › Disulfide-rich domain in A Disintegrin And Metalloprotease (ADAM) domain-containing proteins 0.52 38.0 3.28e-01 82.4% 63.3%
5036498 4.1.1.3 ↗ beta barrels › SH3 › SH3 › SH3 › KOW 0.52 39.0 3.58e-01 88.2% 66.7%
3425721 252.1.1.2 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › DUF7028 0.52 42.0 3.83e-01 100.0% 72.0%
3515117 2004.1.1.73 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.51 41.0 2.83e-01 94.1% 71.0%
4661064 252.1.1.1 ↗ a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.51 38.0 3.67e-01 82.4% 91.5%
None — 0.50 40.0 2.43e-01 94.1% 36.2%
3377905 2004.1.1.73 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.50 40.0 2.70e-01 94.1% 64.0%
D4 medium residues 357-413
PDB
Domain cluster: rep: zinc-ribbon-containing_protein__YP_003407073__Marseillevirus_marseillevirus__694581__D374-426
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24308.2 best DUF7487 52.4 8.80e-14 100.0% 25.9%